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BMRB: 18099

2LM5

Solution structure of Ca2+-CIB1 in complex with the cytoplasmic domain of the integrin aIIb subunit

Authors

Huang, H., Vogel, H.J.

Assembly

CIB1

Entity

1. CIB1 (polymer, Thiol state: all free), 214 monomers, 24469.92 Da Detail

MGHHHHHHHH HHSSGHIDDD DKHMGGSGSR LSKELLAEYQ DLTFLTKQEI LLAHRRFCEL LPQEQRSVES SLRAQVPFEQ ILSLPELKAN PFKERICRVF STSPAKDSLS FEDFLDLLSV FSDTATPDIK SHYAFRIFDF DDDGTLNRED LSRLVNCLTG EGEDTRLSAS EMKQLIDNIL EESDIDRDGT INLSEFQHVI SRSPDFASSF KIVL

2. CA (non-polymer, Thiol state: not present), 40.078 × 2 Da

Total weight

24550.076 Da

Max. entity weight

24469.92 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 86.0 %, Completeness: 45.2 %, Completeness (bb): 70.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	45.2 % (1124 of 2488)	25.7 % (332 of 1292)	64.1 % (626 of 976)	75.5 % (166 of 220)
Backbone	70.2 % (891 of 1270)	44.0 % (189 of 430)	84.7 % (536 of 633)	80.2 % (166 of 207)
Sidechain	28.8 % (410 of 1423)	16.6 % (143 of 862)	48.7 % (267 of 548)	0.0 % (0 of 13)
Aromatic	8.8 % (19 of 216)	10.2 % (11 of 108)	7.4 % (8 of 108)
Methyl	70.4 % (152 of 216)	67.6 % (73 of 108)	73.1 % (79 of 108)

1. CIB1

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
1	CIB1	[U-13C; U-15N; U-2H]	0.5 mM
2	DTT	[U-2H]	5 mM
3	CALCIUM ION	natural abundance	2 mM
4	sodium chloride	natural abundance	100 mM
5	HEPES	natural abundance	50 mM
6	aIIb peptide	natural abundance	0.6 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
9	CIB1	[U-13C; U-2H], I/L/V methyl [1H,13C]	0.5 mM
10	DTT	[U-2H]	5 mM
11	CALCIUM ION	natural abundance	2 mM
12	sodium chloride	natural abundance	100 mM
13	HEPES	natural abundance	50 mM
14	aIIb peptide	natural abundance	0.6 mM
15	D2O	natural abundance	100 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
16	CIB1	[U-10% 13C]	0.5 mM
17	DTT	[U-2H]	5 mM
18	CALCIUM ION	natural abundance	2 mM
19	sodium chloride	natural abundance	100 mM
20	HEPES	natural abundance	50 mM
21	aIIb peptide	natural abundance	0.6 mM
22	D2O	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
23	CIB1	[U-2H], I/L/V methyl [1H,13C]	0.5 mM
24	DTT	[U-2H]	5 mM
25	CALCIUM ION	natural abundance	2 mM
26	sodium chloride	natural abundance	100 mM
27	HEPES	natural abundance	50 mM
28	aIIb peptide	natural abundance	0.6 mM
29	D2O	natural abundance	100 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
30	CIB1	[U-13C; U-15N; U-2H]	0.5 mM
31	DTT	[U-2H]	5 mM
32	CALCIUM ION	natural abundance	2 mM
33	sodium chloride	natural abundance	100 mM
34	HEPES	natural abundance	50 mM
35	aIIb peptide	natural abundance	0.6 mM
36	pf1 phage	natural abundance	14 mg/mL
37	H2O	natural abundance	90 %
38	D2O	natural abundance	10 %

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
39	CIB1	[U-13C; U-15N; U-2H]	0.5 mM
40	DTT	[U-2H]	5 mM
41	CALCIUM ION	natural abundance	2 mM
42	sodium chloride	natural abundance	100 mM
43	HEPES	natural abundance	50 mM
44	aIIb peptide	natural abundance	0.6 mM
45	C12E5/glycerol (0.96/1)	natural abundance	5 %
46	H2O	natural abundance	90 %
47	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.51 ppm, Outliers: 4 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.51 ppm, Outliers: 4 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.2 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2LM5, Strand ID: A Detail

Release date

2012-01-31

Citation

Structural basis for the activation of platelet integrin αIIbβ3 by calcium- and integrin-binding protein 1
Huang, H., Vogel, H.J.
J. Am. Chem. Soc. (2012), 134, 3864-3872, PubMed 22283712 , DOI 10.1021/ja2111306 , Abstract

Related entities 1. CIB1, : 1 : 2 : 8 : 136 entities Detail

Interaction partners 1. CIB1, : 18 interactors Detail

More details for 18 interactors identified by 9 citations

Experiments performed 9 experiments Detail

1 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
1	CIB1	[U-13C; U-15N; U-2H]	0.5 mM
2	DTT	[U-2H]	5 mM
3	CALCIUM ION	natural abundance	2 mM
4	sodium chloride	natural abundance	100 mM
5	HEPES	natural abundance	50 mM
6	aIIb peptide	natural abundance	0.6 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

2 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
1	CIB1	[U-13C; U-15N; U-2H]	0.5 mM
2	DTT	[U-2H]	5 mM
3	CALCIUM ION	natural abundance	2 mM
4	sodium chloride	natural abundance	100 mM
5	HEPES	natural abundance	50 mM
6	aIIb peptide	natural abundance	0.6 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

3 3D HCACO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
1	CIB1	[U-13C; U-15N; U-2H]	0.5 mM
2	DTT	[U-2H]	5 mM
3	CALCIUM ION	natural abundance	2 mM
4	sodium chloride	natural abundance	100 mM
5	HEPES	natural abundance	50 mM
6	aIIb peptide	natural abundance	0.6 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

4 3D HN(COCA)CB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
1	CIB1	[U-13C; U-15N; U-2H]	0.5 mM
2	DTT	[U-2H]	5 mM
3	CALCIUM ION	natural abundance	2 mM
4	sodium chloride	natural abundance	100 mM
5	HEPES	natural abundance	50 mM
6	aIIb peptide	natural abundance	0.6 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

5 3D HNCO type RDC

Instrument

Bruker Avance - 700 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
30	CIB1	[U-13C; U-15N; U-2H]	0.5 mM
31	DTT	[U-2H]	5 mM
32	CALCIUM ION	natural abundance	2 mM
33	sodium chloride	natural abundance	100 mM
34	HEPES	natural abundance	50 mM
35	aIIb peptide	natural abundance	0.6 mM
36	pf1 phage	natural abundance	14 mg/mL
37	H2O	natural abundance	90 %
38	D2O	natural abundance	10 %

6 2D 1H-15N HSQC IPAP

Instrument

Bruker Avance - 700 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
30	CIB1	[U-13C; U-15N; U-2H]	0.5 mM
31	DTT	[U-2H]	5 mM
32	CALCIUM ION	natural abundance	2 mM
33	sodium chloride	natural abundance	100 mM
34	HEPES	natural abundance	50 mM
35	aIIb peptide	natural abundance	0.6 mM
36	pf1 phage	natural abundance	14 mg/mL
37	H2O	natural abundance	90 %
38	D2O	natural abundance	10 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
9	CIB1	[U-13C; U-2H], I/L/V methyl [1H,13C]	0.5 mM
10	DTT	[U-2H]	5 mM
11	CALCIUM ION	natural abundance	2 mM
12	sodium chloride	natural abundance	100 mM
13	HEPES	natural abundance	50 mM
14	aIIb peptide	natural abundance	0.6 mM
15	D2O	natural abundance	100 %

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
16	CIB1	[U-10% 13C]	0.5 mM
17	DTT	[U-2H]	5 mM
18	CALCIUM ION	natural abundance	2 mM
19	sodium chloride	natural abundance	100 mM
20	HEPES	natural abundance	50 mM
21	aIIb peptide	natural abundance	0.6 mM
22	D2O	natural abundance	100 %

9 3D HNCO type RDC

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.5 (±0.1), Details aIIb peptide sequence :Ac-LVLAMWKVGFFKRNRPPLEEDDEEGQ-OH

#	Name	Isotope labeling	Concentration
39	CIB1	[U-13C; U-15N; U-2H]	0.5 mM
40	DTT	[U-2H]	5 mM
41	CALCIUM ION	natural abundance	2 mM
42	sodium chloride	natural abundance	100 mM
43	HEPES	natural abundance	50 mM
44	aIIb peptide	natural abundance	0.6 mM
45	C12E5/glycerol (0.96/1)	natural abundance	5 %
46	H2O	natural abundance	90 %
47	D2O	natural abundance	10 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18099_2lm5.nef
Input source #2: Coordindates	2lm5.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:139:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:188:ASP:OD1	2:2:CA:CA	unknown	unknown	n/a
1:184:ASP:OD2	2:2:CA:CA	unknown	unknown	n/a
1:195:GLU:OE1	2:2:CA:CA	unknown	unknown	n/a
1:145:THR:O	2:1:CA:CA	unknown	unknown	n/a
1:141:ASP:OD2	2:1:CA:CA	unknown	unknown	n/a
1:186:ASP:OD2	2:2:CA:CA	unknown	unknown	n/a
1:143:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:188:ASP:OD2	2:2:CA:CA	unknown	unknown	n/a
1:190:THR:O	2:2:CA:CA	unknown	unknown	n/a
1:150:ASP:OD2	2:1:CA:CA	unknown	unknown	n/a
1:195:GLU:OE2	2:2:CA:CA	unknown	unknown	n/a
1:186:ASP:OD1	2:2:CA:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CA	CALCIUM ION	Distance restraints
B	2	CA	CALCIUM ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-------------------------------10--------20--------30--------40--------50--------60--------70-------
MGHHHHHHHHHHSSGHIDDDDKHMGGSGSRLSKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHHHHHSSGHIDDDDKHMGGSGSRLSKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVF
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------
STSPAKDSLSFEDFLDLLSVFSDTATPDIKSHYAFRIFDFDDDGTLNREDLSRLVNCLTGEGEDTRLSASEMKQLIDNILEESDIDRDGTINLSEFQHVI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
STSPAKDSLSFEDFLDLLSVFSDTATPDIKSHYAFRIFDFDDDGTLNREDLSRLVNCLTGEGEDTRLSASEMKQLIDNILEESDIDRDGTINLSEFQHVI
-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200

180-------190-
SRSPDFASSFKIVL
||||||||||||||
SRSPDFASSFKIVL
-------210----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	214	0	0	100.0

Content subtype: combined_18099_2lm5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	13		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	979		82.7 (chain: A, length: 214)
1	Distance restraints	CNS/XPLOR_distance_constraints_6	Error	14 (1)	undefined	4.7 (chain: A, length: 214), 50.0 (chain: B, length: 2)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	130 (1)	hbond	46.3 (chain: A, length: 214)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	359 (359)	.	86.0 (chain: A, length: 214)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_2	OK	104 (104)	.	48.6 (chain: A, length: 214)
2	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	74 (74)	.	36.4 (chain: A, length: 214)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 214, Sequence coverage: 82.7%
- Total number of assignments
  - ¹³C chemical shifts: 591
  - ¹H chemical shifts: 229
  - ¹⁵N chemical shifts: 159
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	976	591	60.6
¹H chemical shifts	1292	229	17.7
¹⁵N chemical shifts	233	159	68.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	428	350	81.8
¹H chemical shifts	430	159	37.0
¹⁵N chemical shifts	207	159	76.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	548	241	44.0
¹H chemical shifts	862	70	8.1
¹⁵N chemical shifts	26	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	111	77	69.4
¹H chemical shifts	111	70	63.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	108	0	0.0
¹H chemical shifts	108	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_6
- Status: Error
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 214, Sequence coverage: 4.7%
  - Entity_assembly_ID: B, Chain length: 2, Sequence coverage: 50.0%
- Total number of restraints: 14
- Weight of restraints: 1.0 (14)
- Potential type of restraints: square-well-parabolic (14)
- Range of distance target values: 2.17, 3.96 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 214, Sequence coverage: 46.3%
  - Total number of restraints: 130
  - Weight of restraints: 1.0 (130)
  - Potential type of restraints: square-well-parabolic (130)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 214, Sequence coverage: 86.0%
- Total number of restraints: 359
- Total number of restraints per polymer type: 359
- Weight of restraints: 1.0 (359)
- Potential type of restraints: square-well-parabolic (359)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 214, Sequence coverage: 48.6%
- Total number of restraints: 104
- Potential type of restraints: undefined (104)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
- Saveframe: CNS/XPLOR_dipolar_coupling_3
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 214, Sequence coverage: 36.4%
  - Total number of restraints: 74
  - Potential type of restraints: undefined (74)
  - Range of observed RDC values: 100.0, -100.0 (Hz)
  - RDC restraints per residue

Keywords aIIb, alphaIIb, calcium and integrin binding protein, CIB1, integrin, NMR

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Found 1 Document (1.007 seconds)

BMRB: 18099

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. CIB1, : 1 : 2 : 8 : 136 entities Detail

Interaction partners 1. CIB1, : 18 interactors Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 7 contents Detail